Add 3d diffusion model bundle

CONTRIBUTING.md

@@ -84,6 +84,11 @@ In train config file (if exists), please follow the following requirements in or
 
 We prepared several premerge CI tests to verify your bundle.
 
+### Prepare dependencies
+
+For dependencies that support `pip install` command, please put them into `optional_packages_version` in `configs/metadata.json` ([click here for instance](https://github.com/Project-MONAI/model-zoo/blob/dev/models/brats_mri_segmentation/configs/metadata.json)), and the CI test program will extract and install all libraries directly before running tests.
+For dependencies that require multiple steps to install, please prepare a install script in `ci/install_scripts`, and put the bundle name and the script path into `install_dependency_dict` in `ci/bundle_custom_data.py` ([click here for instance](https://github.com/Project-MONAI/model-zoo/tree/dev/ci/install_scripts/)).
+
 ### Necessary verifications
 
 1. Check if necessary files are existing in your bundle.

ci/bundle_custom_data.py

@@ -13,7 +13,12 @@
 # This list is used for our CI tests to determine whether a bundle needs to be tested with
 # the `verify_data_shape` function in `verify_bundle.py`.
 # If a bundle does not need to be tested, please add the bundle name into the list.
-exclude_verify_shape_list = ["mednist_gan", "lung_nodule_ct_detection", "pathology_nuclei_segmentation_classification"]
+exclude_verify_shape_list = [
+    "mednist_gan",
+    "lung_nodule_ct_detection",
+    "pathology_nuclei_segmentation_classification",
+    "brats_mri_generative_diffusion",
+]
 
 # This list is used for our CI tests to determine whether a bundle contains the preferred files.
 # If a bundle does not have any of the preferred files, please add the bundle name into the list.
@@ -30,6 +35,13 @@
     "mednist_reg",
 ]
 
+# This dict is used for our CI tests to install required dependencies that cannot be installed by `pip install` directly.
+# If a bundle has this kind of dependencies, please add the bundle name (key), and the path of the install script (value)
+# into the dict.
+install_dependency_dict = {
+    "brats_mri_generative_diffusion": "ci/install_scripts/install_brats_mri_generative_diffusion_dependency.sh"
+}
+
 # This list is used for our CI tests to determine whether a bundle supports TensorRT export. Related
 # test will be employed for bundles in the list.
 include_verify_tensorrt_list = ["spleen_ct_segmentation", "endoscopic_tool_segmentation", "pathology_tumor_detection"]

ci/install_scripts/install_brats_mri_generative_diffusion_dependency.sh

@@ -0,0 +1,16 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+git clone https://github.com/Project-MONAI/GenerativeModels.git
+cd GenerativeModels/
+git checkout f969c24f88d013dc0045fb7b2885a01fb219992b
+python setup.py install
+cd ..

ci/verify_bundle.py

@@ -11,6 +11,7 @@
 
 import argparse
 import os
+import subprocess
 import sys
 from typing import List
 
@@ -19,6 +20,7 @@
     exclude_verify_preferred_files_list,
     exclude_verify_shape_list,
     exclude_verify_torchscript_list,
+    install_dependency_dict,
 )
 from monai.bundle import ckpt_export, verify_metadata, verify_net_in_out
 from monai.bundle.config_parser import ConfigParser
@@ -47,6 +49,20 @@ def _find_bundle_file(root_dir: str, file: str, suffix=("json", "yaml", "yml")):
     return file_name
 
 
+def _get_weights_names(bundle: str):
+    # TODO: this function is temporarily used. It should be replaced by detailed config tests.
+    if bundle == "brats_mri_generative_diffusion":
+        return "model_autoencoder.pt", "model_autoencoder.ts"
+    return "model.pt", "model.ts"
+
+
+def _get_net_id(bundle: str):
+    # TODO: this function is temporarily used. It should be replaced by detailed config tests.
+    if bundle == "brats_mri_generative_diffusion":
+        return "autoencoder_def"
+    return "network_def"
+
+
 def _check_missing_keys(file_name: str, bundle_path: str, keys_list: List):
     config = ConfigParser.load_config_file(os.path.join(bundle_path, "configs", file_name))
     missing_keys = []
@@ -267,7 +283,9 @@ def verify_data_shape(bundle_path: str, net_id: str, config_file: str):
     )
 
 
-def verify_torchscript(bundle_path: str, net_id: str, config_file: str):
+def verify_torchscript(
+    bundle_path: str, net_id: str, config_file: str, model_name: str = "model.pt", ts_name: str = "model.ts"
+):
     """
     This function is used to verify if the checkpoint is able to export into torchscript model, and
     if "models/model.ts" is provided, it will be checked if it is able to be loaded
@@ -277,21 +295,27 @@ def verify_torchscript(bundle_path: str, net_id: str, config_file: str):
     ckpt_export(
         net_id=net_id,
         filepath=os.path.join(bundle_path, "models/verify_model.ts"),
-        ckpt_file=os.path.join(bundle_path, "models/model.pt"),
+        ckpt_file=os.path.join(bundle_path, "models", model_name),
         meta_file=os.path.join(bundle_path, "configs/metadata.json"),
         config_file=os.path.join(bundle_path, config_file),
         bundle_root=bundle_path,
     )
     print("export weights into TorchScript module successfully.")
 
-    ts_model_path = os.path.join(bundle_path, "models/model.ts")
+    ts_model_path = os.path.join(bundle_path, "models", ts_name)
     if os.path.exists(ts_model_path):
         torch.jit.load(ts_model_path)
         print("Provided TorchScript module is verified correctly.")
 
 
 def verify(bundle, models_path="models", mode="full"):
     print(f"start verifying {bundle}:")
+    # install extra dependencies if needed
+    if bundle in install_dependency_dict.keys():
+        script_path = install_dependency_dict[bundle]
+        install_cmd = f"bash {script_path}"
+        call_status = subprocess.run(install_cmd, shell=True)
+        call_status.check_returncode()
     # add bundle path to ensure custom code can be used
     sys.path = [os.path.join(models_path, bundle)] + sys.path
     # verify bundle directory
@@ -313,7 +337,8 @@ def verify(bundle, models_path="models", mode="full"):
         return
 
     # The following are optional tests and require GPU
-    net_id, inference_file_name = "network_def", _find_bundle_file(os.path.join(bundle_path, "configs"), "inference")
+    net_id = _get_net_id(bundle)
+    inference_file_name = _find_bundle_file(os.path.join(bundle_path, "configs"), "inference")
     config_file = os.path.join("configs", inference_file_name)
 
     if bundle in exclude_verify_shape_list:
@@ -325,7 +350,8 @@ def verify(bundle, models_path="models", mode="full"):
     if bundle in exclude_verify_torchscript_list:
         print(f"bundle: {bundle} does not support torchscript, skip verifying.")
     else:
-        verify_torchscript(bundle_path, net_id, config_file)
+        model_name, ts_name = _get_weights_names(bundle=bundle)
+        verify_torchscript(bundle_path, net_id, config_file, model_name, ts_name)
 
 
 if __name__ == "__main__":

models/brats_mri_generative_diffusion/LICENSE

@@ -0,0 +1,201 @@
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